Whole-Genome Sequencing of a Clinically Isolated Antibiotic-Resistant Enterococcus faecium EntfacYE

Elahi, Yara; Javdani Shahedin, Golshid; Nejati, Ahmad; Ashrafi, Iradj; Asadian, Mahla; Mazaheri Nezhad Fard, Ramin

doi:10.30699/ijmm.15.6.692

year 15, Issue 6 (November - December 2021) Iran J Med Microbiol 2021, 15(6): 692-699 | Back to browse issues page

‎ 10.30699/ijmm.15.6.692

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Elahi Y, Javdani Shahedin G, Nejati A, Ashrafi I, Asadian M, Mazaheri Nezhad Fard R. Whole-Genome Sequencing of a Clinically Isolated Antibiotic-Resistant Enterococcus faecium EntfacYE. Iran J Med Microbiol 2021; 15 (6) :692-699
URL: http://ijmm.ir/article-1-1395-en.html

Whole-Genome Sequencing of a Clinically Isolated Antibiotic-Resistant Enterococcus faecium EntfacYE

Yara Elahi¹

, Golshid Javdani Shahedin²

, Ahmad Nejati³

, Iradj Ashrafi⁴

, Mahla Asadian⁵

, Ramin Mazaheri Nezhad Fard

⁶

1- Department of Genetics, Faculty of Life Sciences, Islamic Azad University Tehran North Branch, Tehran, Iran
2- Pasteur Institute, Tehran, Iran
3- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
4- Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
5- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
6- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran , raminmazaheri@gmail.com

Abstract: (4525 Views)

Background and Objective: Enterococcal infections are considered the most common nosocomial infections. Nowadays, enterococci show high resistance to common antibiotics, especially vancomycin. Vancomycin-resistant Enterococcus faecium is one of the most common nosocomial infections, which is included in the World Health Organization priority pathogens list for research and development of new antibiotics. In this case, we focused on the E. faecium EntfacYE genome and its antibiotic-resistant genes to understand the reasons that caused this bacteria to be resistant to antibiotics.
Materials and Methods: In total, 25 enterococcal samples were isolated from patients' blood. Bacteriophages were isolated on a multidrug-resistant Enterococcus faecium EntfacYE in our previous study. In this study, the isolated E. faecium EntfacYE strain was verified using Sanger partial sequencing of the bacterial elongation factor Tu. EntfacYE strain was assessed for antibiotic resistance, and the bacterial genome was extracted and completely sequenced. The sequenced genome was analyzed, and the genes were annotated in the DNA Data Bank of Japan.
Results: Totally, EntfacYE genome subsystems included 23 various categories with 59 genes belonging to antimicrobial resistance genes, such a way that 49 antibiotic resistance genes were included in specific subsystems, while ten genes lacked specific subsystems. Moreover, cadmium, cobalt, copper, zinc, and mercury resistance genes were identified in the EntfacYE genome.
Conclusion: In conclusion, studies on bacterial genomes help researchers to identify characteristics of common pathogens, including virulence and antibiotic-resistance genes, and hence better understand bacterial pathogenesis to provide novel solutions for the treatment of common infections.

Keywords: Antibiotic resistance, Clinical sample, Enterococcus faecium, Whole-genome Sequencing

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Type of Study: Original Research Article | Subject: Medical Bacteriology
Received: 2021/07/21 | Accepted: 2021/11/1 | ePublished: 2021/12/8

References

1. Gilmore MS, Lebreton F, van Schaik W. Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era. Curr Opin Microbiol. 2013;16(1):10-6. [DOI:10.1016/j.mib.2013.01.006] [PMID] [PMCID]

2. Willems RJ, Top J, Marga van Santen D, Coque TM, Baquero F, Grundmann H, Bonten MJ. Global spread of vancomycin-resistant Enterococcus faecium from distinct nosocomial genetic complex. Emerg Infect Dis. 2005;11(6):821. [DOI:10.3201/1106.041204] [PMID] [PMCID]

3. Arias CA, Murray BE. Emergence and management of drug-resistant enterococcal infections. Expert Rev Anti Infect Ther. 2008;6(5):637-55. [DOI:10.1586/14787210.6.5.637] [PMID]

4. Bonten MJ, Willems R, Weinstein RA. Vancomycin-resistant enterococci: why are they here and where do they come from? Lancet Infect Dis. 2001;1(5):314-25. [DOI:10.1016/S1473-3099(01)00145-1]

5. Benenson S, Cohen MJ, Block C, Stern S, Weiss Y, Moses AE, JIRMI Group. Vancomycin-resistant enterococci in long-term care facilities. Infect Control Hosp Epidemiol. 2009;30(8):786-9. [DOI:10.1086/598345] [PMID]

6. Gruber I, Heudorf U, Werner G, Pfeifer Y, Imirzalioglu C, Ackermann H, Brandt C, Besier S, Wichelhaus TA. Multidrug-resistant bacteria in geriatric clinics, nursing homes and ambulant care-prevalence and risk factors. Int J Med Microbiol Suppl. 2013;303(8):405-9. [DOI:10.1016/j.ijmm.2013.05.002] [PMID]

7. Kos VN, Desjardins CA, Griggs A, Cerqueira G, Van Tonder A, Holden MT, Godfrey P, Palmer KL, Bodi K, Mongodin EF, Wortman J. Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States. MBio. 2012;3(3). [DOI:10.1128/mBio.00112-12]

8. Brodrick HJ, Raven KE, Harrison EM, Blane B, Reuter S, Torok ME, Parkhill J, Peacock SJ. Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network. Genome Med. 2016;8(1):1-9. [DOI:10.1186/s13073-015-0259-7] [PMID] [PMCID]

9. Kim EB, Marco ML. Nonclinical and clinical Enterococcus faecium strains, but not Enterococcus faecalis strains, have distinct structural and functional genomic features. Appl Environ Microbiol. 2014;80(1):154-65. [DOI:10.1128/AEM.03108-13] [PMID] [PMCID]

10. Arias CA, Murray BE. The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol. 2012;10(4):266-78. [DOI:10.1038/nrmicro2761] [PMID] [PMCID]

11. Palmer KL, Gilmore MS. Multidrug-resistant enterococci lack CRISPR-cas. MBio. 2010;1(4). [DOI:10.1128/mBio.00227-10] [PMID] [PMCID]

12. Elahi Y, Nowroozi J, Fard RM. Isolation and characterization of bacteriophages from wastewater sources on Enterococcus spp. isolated from clinical samples. Iran J Microbiol. 2021;13(5):671-7. [DOI:10.18502/ijm.v13i5.7434]

13. Adeniji OO, Sibanda T, Okoh AI. Recreational water quality status of the Kidd's Beach as determined by its physicochemical and bacteriological quality parameters. Heliyon. 2019;5(6):e01893. [DOI:10.1016/j.heliyon.2019.e01893] [PMID] [PMCID]

14. Wang Y, Oppong TB, Liang X, Duan G, Yang H. Methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci co-colonization in patients: A meta-analysis. Am J Infect Control. 2019;48(8):925-932. [DOI:10.1016/j.ajic.2019.11.010] [PMID]

15. El Jeni R, Ghedira K, El Bour M, Abdelhak S, Benkahla A, Bouhaouala-Zahar B. High-quality genome sequence assembly of R. A73 Enterococcus faecium isolated from freshwater fish mucus. BMC Microbiol. 2020;20(1):1-2. [DOI:10.1186/s12866-020-01980-8] [PMID] [PMCID]

16. Shokoohizadeh L, Ekrami A, Labibzadeh M, Ali L, Alavi SM. Antimicrobial resistance patterns and virulence factors of enterococci isolates in hospitalized burn patients. BMC Research Notes. 2018;11(1):1-5. [DOI:10.1186/s13104-017-3088-5] [PMID] [PMCID]

17. Hosseini MJ, Sadripour R. Antibiotic resistance pattern of bacteria isolated from nosocomial infection in internal surgery and neurosurgery intensive care unit (NICU) at a tertiary care hospital in Tehran, Iran. Biosci Biotechnol Res Asia. 2017;14(3):1095-102. [DOI:10.13005/bbra/2547]

18. Leong KW, Cooley LA, Anderson TL, Gautam SS, McEwan B, Wells A, Wilson F, Hughson L, O'Toole RF. Emergence of vancomycin-resistant Enterococcus faecium at an Australian hospital: a whole genome sequencing analysis. Sci Rep. 2018;8(1):1-1. [DOI:10.1038/s41598-018-24614-6] [PMID] [PMCID]

19. Lytsy B, Engstrand L, Gustafsson Å, Kaden R. Time to review the gold standard for genotyping vancomycin-resistant enterococci in epidemiology: comparing whole-genome sequencing with PFGE and MLST in three suspected outbreaks in Sweden during 2013-2015. Infect Genet Evol. 2017;54:74-80. [DOI:10.1016/j.meegid.2017.06.010] [PMID]

20. Akpaka PE, Kissoon S, Jayaratne P, Wilson C, Golding GR, Nicholson AM, Lewis DB, Hermelijn SM, Wilson-Pearson A, Smith A. Genetic characteristics and molecular epidemiology of vancomycin-resistant enterococci isolates from Caribbean countries. PloS One. 2017;12(10):e0185920. [DOI:10.1371/journal.pone.0185920] [PMID] [PMCID]

21. Shahraki S, Rabi Nezhad Mousavi M. Determination of virulence factors in clinical multidrug resistance enterococci isolates at southeast of Iran. Jundishapur J Microbiol. 2017;10(5). [DOI:10.5812/jjm.45514]

22. Arbabi L, Boustanshenas M, Rahbar M, Owlia P, Adabi M, Koohi SR, Afshar M, Fathizadeh S, Majidpour A, Talebi-Taher M. Antibiotic susceptibility pattern and virulence genes in Enterococcus spp. isolated from clinical samples of Milad hospital of Tehran, Iran. Arch Clin Infect Dis. 2016;11(3). [DOI:10.5812/archcid.36260]

23. Seppälä H, Skurnik M, Soini H, Roberts MC, Huovinen P. A novel erythromycin resistance methylase gene (ermTR) in Streptococcus pyogenes. Antimicrob Agents Chemother. 1998;42(2):257-62. [DOI:10.1128/AAC.42.2.257] [PMID] [PMCID]

24. Ahmadpoor N, Ahmadrajabi R, Esfahani S, Hojabri Z, Moshafi MH, Saffari F. High-level resistance to erythromycin and tetracycline and dissemination of resistance determinants among clinical enterococci in Kerman-Iran. Med Princ Pract. 2021; Mar 31. Online ahead of print. [DOI:10.1159/000516216] [PMID] [PMCID]

25. Kristich CJ, Rice LB, Arias CA. Enterococcal infection-treatment and antibiotic resistance. In: Enterococci: From commensals to leading causes of drug resistant infection. Boston: Massachusetts Eye and Ear Infirmary; 2014.

26. Jeong DW, Lee B, Heo S, Oh Y, Heo G, Lee JH. Two genes involved in clindamycin resistance of Bacillus licheniformis and Bacillus paralicheniformis identified by comparative genomic analysis. PloS One. 2020;15(4):e0231274. [DOI:10.1371/journal.pone.0231274] [PMID] [PMCID]

27. Rengaraj R, Mariappan S, Sekar U, Kamalanadhan A. Detection of vancomycin resistance among Enterococcus faecalis and Staphylococcus aureus. Journal of clinical and diagnostic research: JCDR. 2016;10(2):DC04. [DOI:10.7860/JCDR/2016/17552.7201] [PMID] [PMCID]

28. Zavaryani SM, Mirnejad R, Piranfar V, Moghaddam MM, Sajjadi N, Saeedi S. Assessment of susceptibility to five common antibiotics and their resistance pattern in clinical Enterococcus isolates. IJP. 2020;15(2):96. [DOI:10.30699/ijp.2020.114009.2236] [PMID] [PMCID]

29. Soltani Nezhad S, Rabbani Khorasgani M, Emtiazi G. Analysis of zinc resistance gene in zinc and zinc oxide nanoparticles resistant Pseudomonas stutzeri SEE-1 isolated from soil. JMW. 2015;8(23):139-47.

30. Guo H, Luo S, Chen L, Xiao X, Xi Q, Wei W, Zeng G, Liu C, Wan Y, Chen J, He Y. Bioremediation of heavy metals by growing hyperaccumulaor endophytic bacterium Bacillus sp. L14. Bioresour Technol. 2010;101(22):8599-605. [DOI:10.1016/j.biortech.2010.06.085] [PMID]

31. Shirdam R, Khanafari A, Tabatabaei A. Cadmium, nickel and vanadium accumulation by three strains of marine bacteria. Iran J Biotechnol. 2006;3(4):180-7.

32. Li C, Li Y, Ding C. The role of copper homeostasis at the host-pathogen axis: from bacteria to fungi. Int J Mol Sci. 2019;20(1):175. [DOI:10.3390/ijms20010175] [PMID] [PMCID]

33. Nami Y, Vaseghi Bakhshayesh R, Mohammadzadeh Jalaly H, Lotfi H, Eslami S, Hejazi MA. Probiotic properties of Enterococcus isolated from artisanal dairy products. Front Microbiol. 2019;10:300. [DOI:10.3389/fmicb.2019.00300] [PMID] [PMCID]

34. Lavova M, Bezekova J, Canigova M, Krocko M, Domig K. Species identification of enterococci by biochemical test and molecular-genetic methods. Potravinarstvo. 2014;8(1):124-9. [DOI:10.5219/364]